10 results on '"Najnin T"'
Search Results
2. Single TRAM domain RNA-binding proteins in Archaea: functional insight from Ctr3 from the Antarctic methanogen Methanococcoides burtonii
- Author
-
Taha, Siddiqui, KS, Campanaro, S, Najnin, T, Deshpande, N, Williams, TJ, Aldrich-Wright, J, Wilkins, M, Curmi, PMG, Cavicchioli, R, Taha, Siddiqui, KS, Campanaro, S, Najnin, T, Deshpande, N, Williams, TJ, Aldrich-Wright, J, Wilkins, M, Curmi, PMG, and Cavicchioli, R
- Abstract
TRAM domain proteins present in Archaea and Bacteria have a β-barrel shape with anti-parallel β-sheets that form a nucleic acid binding surface; a structure also present in cold shock proteins (Csps). Aside from protein structures, experimental data defining the function of TRAM domains is lacking. Here, we explore the possible functional properties of a single TRAM domain protein, Ctr3 (cold-responsive TRAM domain protein 3) from the Antarctic archaeon Methanococcoides burtonii that has increased abundance during low temperature growth. Ribonucleic acid (RNA) bound by Ctr3 in vitro was determined using RNA-seq. Ctr3-bound M. burtonii RNA with a preference for transfer (t)RNA and 5S ribosomal RNA, and a potential binding motif was identified. In tRNA, the motif represented the C loop; a region that is conserved in tRNA from all domains of life and appears to be solvent exposed, potentially providing access for Ctr3 to bind. Ctr3 and Csps are structurally similar and are both inferred to function in low temperature translation. The broad representation of single TRAM domain proteins within Archaea compared with their apparent absence in Bacteria, and scarcity of Csps in Archaea but prevalence in Bacteria, suggests they represent distinct evolutionary lineages of functionally equivalent RNA-binding proteins.
- Published
- 2016
3. Characterization of a temperature-responsive two component regulatory system from the Antarctic archaeon, Methanococcoides burtonii
- Author
-
Najnin, T, Siddiqui, KS, Taha, Elkaid, N, Kornfeld, G, Curmi, PMG, Cavicchioli, R, Najnin, T, Siddiqui, KS, Taha, Elkaid, N, Kornfeld, G, Curmi, PMG, and Cavicchioli, R
- Abstract
Cold environments dominate the Earth's biosphere and the resident microorganisms play critical roles in fulfilling global biogeochemical cycles. However, only few studies have examined the molecular basis of thermosensing; an ability that microorganisms must possess in order to respond to environmental temperature and regulate cellular processes. Two component regulatory systems have been inferred to function in thermal regulation of gene expression, but biochemical studies assessing these systems in Bacteria are rare, and none have been performed in Archaea or psychrophiles. Here we examined the LtrK/LtrR two component regulatory system from the Antarctic archaeon, Methanococcoides burtonii, assessing kinase and phosphatase activities of wild-type and mutant proteins. LtrK was thermally unstable and had optimal phosphorylation activity at 10 °C (the lowest optimum activity for any psychrophilic enzyme), high activity at 0 °C and was rapidly thermally inactivated at 30 °C. These biochemical properties match well with normal environmental temperatures of M. burtonii (0-4 °C) and the temperature this psychrophile is capable of growing at in the laboratory (-2 to 28 °C). Our findings are consistent with a role for LtrK in performing phosphotransfer reactions with LtrR that could lead to temperature-dependent gene regulation.
- Published
- 2016
4. Single TRAM domain RNA-binding proteins in A rchaea: functional insight from Ctr3 from the Antarctic methanogen M ethanococcoides burtonii.
- Author
-
Taha, Siddiqui, K. S., Campanaro, S., Najnin, T., Deshpande, N., Williams, T. J., Aldrich ‐ Wright, J., Wilkins, M., Curmi, P. M. G., and Cavicchioli, R.
- Subjects
METHANOGENS ,RNA-binding proteins ,COLD shock proteins ,BACTERIAL protein structure - Abstract
TRAM domain proteins present in A rchaea and Bacteria have a β-barrel shape with anti-parallel β-sheets that form a nucleic acid binding surface; a structure also present in cold shock proteins ( Csps). Aside from protein structures, experimental data defining the function of TRAM domains is lacking. Here, we explore the possible functional properties of a single TRAM domain protein, Ctr3 ( cold-responsive TRAM domain protein 3) from the Antarctic archaeon M ethanococcoides burtonii that has increased abundance during low temperature growth. Ribonucleic acid ( RNA) bound by Ctr3 in vitro was determined using RNA-seq. Ctr3-bound M . burtonii RNA with a preference for transfer (t) RNA and 5S ribosomal RNA, and a potential binding motif was identified. In t RNA, the motif represented the C loop; a region that is conserved in t RNA from all domains of life and appears to be solvent exposed, potentially providing access for Ctr3 to bind. Ctr3 and Csps are structurally similar and are both inferred to function in low temperature translation. The broad representation of single TRAM domain proteins within A rchaea compared with their apparent absence in B acteria, and scarcity of Csps in A rchaea but prevalence in B acteria, suggests they represent distinct evolutionary lineages of functionally equivalent RNA-binding proteins. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
5. Corrigendum: Characterization of a temperature-responsive two component regulatory system from the Antarctic archaeon, Methanococcoides burtonii.
- Author
-
Najnin, T., Siddiqui, K. S., Taha, Elkaid, N., Kornfeld, G., Curmi, P. M. G., and Cavicchioli, R.
- Published
- 2016
- Full Text
- View/download PDF
6. Characterization of a temperature-responsive two component regulatory system from the Antarctic archaeon, Methanococcoides burtonii.
- Author
-
Najnin, T., Siddiqui, K. S., Taha, Elkaid, N., Kornfeld, G., Curmi, P. M. G., and Cavicchioli, R.
- Published
- 2016
- Full Text
- View/download PDF
7. A Network-Based Approach for Improving Annotation of Transcription Factor Functions and Binding Sites in Arabidopsis thaliana .
- Author
-
Najnin T, Saimon SH, Sunter G, and Ruan J
- Subjects
- Transcription Factors genetics, Gene Expression Regulation, Gene Regulatory Networks, Binding Sites genetics, Arabidopsis genetics
- Abstract
Transcription factors are an integral component of the cellular machinery responsible for regulating many biological processes, and they recognize distinct DNA sequence patterns as well as internal/external signals to mediate target gene expression. The functional roles of an individual transcription factor can be traced back to the functions of its target genes. While such functional associations can be inferred through the use of binding evidence from high-throughput sequencing technologies available today, including chromatin immunoprecipitation sequencing, such experiments can be resource-consuming. On the other hand, exploratory analysis driven by computational techniques can alleviate this burden by narrowing the search scope, but the results are often deemed low-quality or non-specific by biologists. In this paper, we introduce a data-driven, statistics-based strategy to predict novel functional associations for transcription factors in the model plant Arabidopsis thaliana . To achieve this, we leverage one of the largest available gene expression compendia to build a genome-wide transcriptional regulatory network and infer regulatory relationships among transcription factors and their targets. We then use this network to build a pool of likely downstream targets for each transcription factor and query each target pool for functionally enriched gene ontology terms. The results exhibited sufficient statistical significance to annotate most of the transcription factors in Arabidopsis with highly specific biological processes. We also perform DNA binding motif discovery for transcription factors based on their target pool. We show that the predicted functions and motifs strongly agree with curated databases constructed from experimental evidence. In addition, statistical analysis of the network revealed interesting patterns and connections between network topology and system-level transcriptional regulation properties. We believe that the methods demonstrated in this work can be extended to other species to improve the annotation of transcription factors and understand transcriptional regulation on a system level.
- Published
- 2023
- Full Text
- View/download PDF
8. Diverse Sensory Repertoire of Paralogous Chemoreceptors Tlp2, Tlp3, and Tlp4 in Campylobacter jejuni .
- Author
-
Taha, Elgamoudi BA, Andrianova EP, Haselhorst T, Day CJ, Hartley-Tassell LE, King RM, Najnin T, Zhulin IB, and Korolik V
- Subjects
- Humans, Ligands, Molecular Docking Simulation, Phylogeny, Chemotaxis, Bacterial Proteins genetics, Bacterial Proteins metabolism, Campylobacter jejuni genetics
- Abstract
Campylobacter jejuni responds to extracellular stimuli via transducer-like chemoreceptors (Tlps). Here, we describe receptor-ligand interactions of a unique paralogue family of dCache_1 (double Ca lcium channels and che motaxis) chemoreceptors: Tlp2, Tlp3, and Tlp4. Phylogenetic analysis revealed that Tlp2, Tlp3, and Tlp4 receptors may have arisen through domain duplications, followed by a divergent evolutionary drift, with Tlp3 emerging more recently, and unexpectedly, responded to glycans, as well as multiple organic and amino acids with overlapping specificities. All three Tlps interacted with five monosaccharides and complex glycans, including Lewis's antigens, P antigens, and fucosyl GM1 ganglioside, indicating a potential role in host-pathogen interactions. Analysis of chemotactic motility of single, double, and triple mutants indicated that these chemoreceptors are likely to work together to balance responses to attractants and repellents to modulate chemotaxis in C. jejuni. Molecular docking experiments, in combination with saturation transfer difference nuclear magnetic resonance spectroscopy and competition surface plasmon resonance analysis, illustrated that the ligand-binding domain of Tlp3 possess one major binding pocket with two overlapping, but distinct binding sites able to interact with multiple ligands. A diverse sensory repertoire could provide C. jejuni with the ability to modulate responses to attractant and repellent signals and allow for adaptation in host-pathogen interactions. IMPORTANCE Campylobacter jejuni responds to extracellular stimuli via transducer-like chemoreceptors (Tlps). This remarkable sensory perception mechanism allows bacteria to sense environmental changes and avoid unfavorable conditions or to maneuver toward nutrient sources and host cells. Here, we describe receptor-ligand interactions of a unique paralogue family of chemoreceptors, Tlp2, Tlp3, and Tlp4, that may have arisen through domain duplications, followed by a divergent evolutionary drift, with Tlp3 emerging more recently. Unlike previous reports of ligands interacting with sensory proteins, Tlp2, Tlp3, and Tlp4 responded to many types of chemical compounds, including simple and complex sugars such as those present on human blood group antigens and gangliosides, indicating a potential role in host-pathogen interactions. Diverse sensory repertoire could provide C. jejuni with the ability to modulate responses to attractant and repellent signals and allow for adaptation in host-pathogen interactions.
- Published
- 2022
- Full Text
- View/download PDF
9. A Robust Personalized Classification Method for Breast Cancer Metastasis Prediction.
- Author
-
Adnan N, Najnin T, and Ruan J
- Abstract
Accurate prediction of breast cancer metastasis in the early stages of cancer diagnosis is crucial to reduce cancer-related deaths. With the availability of gene expression datasets, many machine-learning models have been proposed to predict breast cancer metastasis using thousands of genes simultaneously. However, the prediction accuracy of the models using gene expression often suffers from the diverse molecular characteristics across different datasets. Additionally, breast cancer is known to have many subtypes, which hinders the performance of the models aimed at all subtypes. To overcome the heterogeneous nature of breast cancer, we propose a method to obtain personalized classifiers that are trained on subsets of patients selected using the similarities between training and testing patients. Results on multiple independent datasets showed that our proposed approach significantly improved prediction accuracy compared to the models trained on the complete training dataset and models trained on specific cancer subtypes. Our results also showed that personalized classifiers trained on positively and negatively correlated patients outperformed classifiers trained only on positively correlated patients, highlighting the importance of selecting proper patient subsets for constructing personalized classifiers. Additionally, our proposed approach obtained more robust features than the other models and identified different features for different patients, making it a promising tool for designing personalized medicine for cancer patients.
- Published
- 2022
- Full Text
- View/download PDF
10. A direct-sensing galactose chemoreceptor recently evolved in invasive strains of Campylobacter jejuni.
- Author
-
Day CJ, King RM, Shewell LK, Tram G, Najnin T, Hartley-Tassell LE, Wilson JC, Fleetwood AD, Zhulin IB, and Korolik V
- Subjects
- Amino Acid Sequence, Animals, Bacterial Proteins metabolism, Calcium-Binding Proteins metabolism, Campylobacter Infections microbiology, Campylobacter jejuni pathogenicity, Chemotaxis genetics, Chickens, Galactose metabolism, Humans, Monosaccharide Transport Proteins metabolism, Mutation, Periplasmic Binding Proteins metabolism, Protein Binding, Sequence Homology, Amino Acid, Virulence genetics, Bacterial Proteins genetics, Calcium-Binding Proteins genetics, Campylobacter jejuni genetics, Monosaccharide Transport Proteins genetics, Periplasmic Binding Proteins genetics
- Abstract
A rare chemotaxis receptor, Tlp11, has been previously identified in invasive strains of Campylobacter jejuni, the most prevalent cause of bacterial gastroenteritis worldwide. Here we use glycan and small-molecule arrays, as well as surface plasmon resonance, to show that Tlp11 specifically interacts with galactose. Tlp11 is required for the chemotactic response of C. jejuni to galactose, as shown using wild type, allelic inactivation and addition mutants. The inactivated mutant displays reduced virulence in vivo, in a model of chicken colonization. The Tlp11 sensory domain represents the first known sugar-binding dCache_1 domain, which is the most abundant family of extracellular sensors in bacteria. The Tlp11 signalling domain interacts with the chemotaxis scaffolding proteins CheV and CheW, and comparative genomic analysis indicates a likely recent evolutionary origin for Tlp11. We propose to rename Tlp11 as CcrG, Campylobacter ChemoReceptor for Galactose.
- Published
- 2016
- Full Text
- View/download PDF
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.